Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ATF4

Cell type

Cell type Class
Blood
Cell type
HUDEP-2
NA
NA

Attributes by original data submitter

Sample

source_name
erythroid progenitor cells
cell type
umbilical cord derived erythroid progenitor cells
cell line
HUDEP-2
genotype/variation
WT
antibody
rabbit anti-ATF4 (CST 11815S)
Stage
Undifferentiated

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10 million cells per sample were harvested and cross-linked in 1% Formaldehyde. Cross-linking was quenched with the addition of 1.5M glycine. Samples were then lysed for 10 minutes at 4C in 50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100. Cells were then centrifuged at 1500g for 3 minutes and the supernatant was discarded. The pellet was resuspended in 10 mM Tris–HCl, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA and incubated for 5 minutes at 4C. The cells were then centrifuged at 1500g for 3 minutes and the supernatant was discarded. The pellet was resuspended in 10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine and sonicated using the Covaris S220 following manufacturer's instructions. Protein A beads (ThermoFisher) were complexed with antibody and the antibody-bead complexes were incubated with cell lysates at 4C overnight with rotation. The antibodies used were rabbit anti-ATF4 (CST 11815S) and rabbit IgG (Novus Biologicals NBP2-24891). The beads were retrieved using a magnetic stand and rinsed with RIPA buffer. Elution buffer containing 50 mM Tris–HCl, pH 8; 10 mM EDTA; 1% SDS was added to the beads for reverse crosslinking at 65C overnight with shaking. After reverse crosslinking, the beads were removed. The eluted DNA was treated with RNaseA and Proteinase K and then purified using Qiagen MinElute PCR Purification Kit, following the manufacturer's instructions. Sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7647) and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) following manufacturer's instructions. Paired-end 150bp reads were generated on an Illumina NextSeq500 at the Functional Genomics Center Zürich (FGCZ) and demultiplexed.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
53044681
Reads aligned (%)
163.2
Duplicates removed (%)
12.5
Number of peaks
846 (qval < 1E-05)

hg38

Number of total reads
53044681
Reads aligned (%)
165.3
Duplicates removed (%)
12.1
Number of peaks
1731 (qval < 1E-05)

Base call quality data from DBCLS SRA